The Whitecaps jumped out to a 1-0 lead on Sunday when Bojarski doubled home Perez in the first inning.
Burlington responded however with four runs of their own in the second inning.
In the third inning, West Michigan scored three runs when Wenceel Perez hit a solo home run, Nick Ames singled home John Valente and Jeremiah Burks snigled home Bojarski.
The Whitecaps took a 5-4 lead in the sixth inning when Bojarski hit a solo home run.
The lead was short lived as Burlington scored five runs in the bottom of the seventh to ultimately win 9-5.
With the loss, the Whitecaps fall to 13-15 overall on the season and are three and a half games behind Great Lakes for first place in the Midwest League Eastern Division.
On Monday, the Whitecaps will return home to start a three game series with Peoria at 7:05 p.m.